The team said in a statement that fellow crew members were the only other people on board the yacht Iroquois, which was at Rowes Wharf near the financial district and is a sight familiar to Bostonians.
The man was 28 to 30 years old, said police spokeswoman Cheryl Fiandaca. When firefighters and police arrived at the yacht, they found him in cardiac arrest, and attempts to revive him were unsuccessful.
It wasn't clear who called authorities, and police did not release the man's name. The manner of death also wasn't released.
Police at the scene did not comment, and a man who appeared to be a yacht crew member said he could not comment.
"Mr. Henry and the members of the Boston Red Sox are saddened by the news and send deepest condolences to his family," the team's statement said.
Henry, the team's principal owner, has owned the Red Sox with two major partners since 2002 and is a former owner of the Florida Marlins. He is chairman of John W. Henry & Co. Inc., a hedge fund he founded in 1981.
The team has won two World Series during his tenure, the first in 2004 after an 84-year title drought.
Henry is also the principal owner of English soccer team Liverpool FC.
Forbes magazine reported in 2011 that Henry had listed the 164-foot yacht for sale for $28 million.
Associated Press writers Steve LeBlanc and Jay Lindsay contributed to this report.Suggest a correction